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10x Genomics
Visium Spatial Gene Expression

Sequencing - Read 2 Length

Visium gene expression & targeted

10x recommends sequencing read 2 to a length of 90 bases.

Space Ranger from v1.1 onwards is less sensitive than previous versions to read length effects. In our experience, the rate at which reads map confidently to a gene, as well as the sensitivity of the resulting analysis, is consistent across a range of read lengths longer than 70 bp. The following graph shows the relationship between read mapping and read 2 length, after trimming, for six representative samples.

Mapped reads is consistent across read lengths over 70 bp after trimming

mapped reads versus read length

Visium for FFPE

10x Genomics recommends sequencing read 2 to a length of 50 bases.

For formalin fixed paraffin embedded (FFPE) tissue the construct is of a known length. Since the reads are aligned to the reference, read 2 length shorter than 50 bases can lead to decreased performance.

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